def misalign_pet(workflow, inputnode, pet2mri):
###Create rotation xfm files based on transform error
transformNode = pe.Node(interface=rsl.param2xfmInterfaceCommand(),
name='transformNode')
workflow.connect(inputnode, 'error', transformNode, 'transformation')
### Concatenate pet2mri and misalignment xfm
pet2misalign_xfm = pe.Node(interface=ConcatCommand(),
name="pet2misalign_xfm")
workflow.connect(pet2mri, 'out_file_xfm', pet2misalign_xfm, 'in_file')
workflow.connect(transformNode, 'out_file', pet2misalign_xfm, 'in_file_2')
###Apply transformation to PET file
transform_resampleNode = pe.Node(interface=rsl.ResampleCommand(),
name="transform_resampleNode")
transform_resampleNode.inputs.use_input_sampling = True
workflow.connect(transformNode, 'out_file', transform_resampleNode,
'transformation')
workflow.connect(pet2mri, 'out_file_img', transform_resampleNode,
'in_file')
###Rotate brain mask
transform_brainmaskNode = pe.Node(interface=rsl.ResampleCommand(),
name="transform_brainmaskNode")
transform_brainmaskNode.inputs.interpolation = 'nearest_neighbour'
workflow.connect(pet2misalign_xfm, 'out_file', transform_brainmaskNode,
'transformation')
workflow.connect(transform_resampleNode, 'out_file',
transform_brainmaskNode, 'model_file')
invert_concat_pet2misalign_xfm = pe.Node(
interface=minc.XfmInvert(), name="invert_concat_pet2misalign_xfm")
workflow.connect(pet2misalign_xfm, 'out_file',
invert_concat_pet2misalign_xfm, 'input_file')
pet2mri = final_pet2mri = pe.Node(interface=niu.IdentityInterface(
fields=["out_file_img", "out_file_xfm", "out_file_xfm_invert"]),
name="pet2mri_misaligned")
workflow.connect(transform_resampleNode, "out_file", final_pet2mri,
"out_file_img")
workflow.connect(pet2misalign_xfm, "out_file", final_pet2mri,
"out_file_xfm")
workflow.connect(invert_concat_pet2misalign_xfm, "output_file",
final_pet2mri, "out_file_xfm_invert")
t1_brain_mask_img = 'out_file'
def get_workflow(name, infosource, opts):
'''
Create workflow to perform PET to T1 co-registration.
1. PET to T1 coregistration with brain masks
2. PET to T1 coregistration without brain masks (OPTIONAL)
3. Transform T1 MRI brainmask and headmask from MNI 152 to T1 native
4. Resample 4d PET image to T1 space
5. Resample 4d PET image to MNI 152 space
:param name: Name for workflow
:param infosource: Infosource for basic variables like subject id (sid) and condition id (cid)
:param datasink: Node in which output data is sent
:param opts: User options
:returns: workflow
'''
workflow = pe.Workflow(name=name)
#Define input node that will receive input from outside of workflow
inputnode = pe.Node(niu.IdentityInterface(fields=["pet_volume","pet_volume_4d","nativeT1nuc","t1_headMask","tka_label_img_t1","results_label_img_t1","pvc_label_img_t1", "t1_brain_mask", "xfmT1MNI", "T1Tal", "error", "header" ]), name='inputnode')
#Define empty node for output
outputnode = pe.Node(niu.IdentityInterface(fields=["petmri_img", "petmri_img_4d","petmni_img_4d","petmri_xfm","mripet_xfm",'petmni_xfm', 'mnipet_xfm' ]), name='outputnode')
node_name="pet_brainmask"
petMasking = pe.Node(interface=PETheadMasking(), name=node_name)
petMasking.inputs.slice_factor = opts.slice_factor
petMasking.inputs.total_factor = opts.total_factor
workflow.connect(inputnode, 'pet_volume', petMasking, 'in_file')
workflow.connect(inputnode, 'header', petMasking, 'in_json')
#node_name="pet2mri_withMask"
#pet2mri_withMask = pe.Node(interface=PETtoT1LinRegRunning(), name=node_name)
#pet2mri_withMask.inputs.clobber = True
#pet2mri_withMask.inputs.verbose = opts.verbose
#pet2mri_withMask.inputs.lsq="lsq6"
#if opts.no_mask :
node_name="pet2mri"
pet2mri = pe.Node(interface=PETtoT1LinRegRunning(), name=node_name)
pet2mri.inputs.clobber = True
pet2mri.inputs.verbose = opts.verbose
pet2mri.inputs.lsq="lsq6"
pet2mri.inputs.metric="mi"
#else :
#pet2mri = pet2mri_withMask
final_pet2mri = pet2mri
if isdefined(inputnode.inputs.error) :
final_pet2mri.inputs.error = error
node_name="t1_brain_mask_pet-space"
pet_brain_mask = pe.Node(interface=minc.Resample(), name=node_name)
pet_brain_mask.inputs.nearest_neighbour_interpolation = True
pet_brain_mask.inputs.clobber = True
pet_brain_mask_img = 'output_file'
workflow.connect([(inputnode, pet_brain_mask, [('t1_brain_mask', 'input_file' )]),
(inputnode, pet_brain_mask, [('pet_volume', 'like')]),
(pet2mri, pet_brain_mask, [('out_file_xfm_invert', 'transformation')])
])
if opts.calculate_t1_pet_space :
t1_pet_space = pe.Node(interface=minc.Resample(), name="t1_pet_space")
t1_pet_space.inputs.clobber = True
workflow.connect([(inputnode, t1_pet_space, [('nativeT1nuc', 'input_file' )]),
(inputnode, t1_pet_space, [('pet_volume', 'like')]),
(pet2mri, t1_pet_space, [('out_file_xfm_invert', 'transformation')])
])
#if opts.no_mask :
workflow.connect([(inputnode, pet2mri, [('pet_volume', 'in_source_file')]),
(inputnode, pet2mri, [('nativeT1nuc', 'in_target_file')])#,
#(petMasking, pet2mri, [('out_file', 'in_source_mask')]),
#(inputnode, pet2mri, [('pet_volume', 'init_file_xfm')])
#(pet2mri_withMask, pet2mri, [('out_file_xfm', 'init_file_xfm')])
])
#workflow.connect([(inputnode, pet2mri_withMask, [('pet_volume', 'in_source_file')]),
#(petMasking, pet2mri_withMask, [('out_file', 'in_source_mask')]),
#(inputnode, pet2mri_withMask, [('nativeT1nuc', 'in_target_file')])
#])
#if opts.coregistration_brain_mask :
#workflow.connect(inputnode, 't1_brain_mask', pet2mri_withMask, 'in_target_mask')
#workflow.connect(inputnode, 't1_brain_mask', pet2mri, 'in_target_mask')
if opts.test_group_qc :
###Create rotation xfm files based on transform error
transformNode = pe.Node(interface=rsl.param2xfmInterfaceCommand(), name='transformNode')
workflow.connect(inputnode, 'error', transformNode, 'transformation')
### Concatenate pet2mri and misalignment xfm
pet2misalign_xfm=pe.Node(interface=ConcatCommand(), name="pet2misalign_xfm")
workflow.connect(pet2mri,'out_file_xfm', pet2misalign_xfm, 'in_file')
workflow.connect(transformNode,'out_file', pet2misalign_xfm, 'in_file_2')
###Apply transformation to PET file
transform_resampleNode=pe.Node(interface=rsl.ResampleCommand(),name="transform_resampleNode")
transform_resampleNode.inputs.use_input_sampling=True;
workflow.connect(transformNode, 'out_file', transform_resampleNode, 'transformation')
workflow.connect(pet2mri, 'out_file_img', transform_resampleNode, 'in_file')
#workflow.connect(pet2misalign_xfm, 'out_file', transform_resampleNode, 'transformation')
###Rotate brain mask
transform_brainmaskNode=pe.Node(interface=rsl.ResampleCommand(), name="transform_brainmaskNode" )
transform_brainmaskNode.inputs.interpolation='nearest_neighbour'
workflow.connect(pet2misalign_xfm, 'out_file', transform_brainmaskNode, 'transformation')
workflow.connect(transform_resampleNode, 'out_file', transform_brainmaskNode, 'model_file')
workflow.connect(pet_brain_mask, pet_brain_mask_img, transform_brainmaskNode, 'in_file')
invert_concat_pet2misalign_xfm=pe.Node(interface=minc.XfmInvert(),name="invert_concat_pet2misalign_xfm")
workflow.connect(pet2misalign_xfm,'out_file',invert_concat_pet2misalign_xfm,'input_file')
pet2mri = final_pet2mri = pe.Node(interface=niu.IdentityInterface(fields=["out_file_img", "out_file_xfm", "out_file_xfm_invert"]), name="pet2mri_misaligned")
workflow.connect(transform_resampleNode, "out_file", final_pet2mri, "out_file_img")
workflow.connect(pet2misalign_xfm, "out_file", final_pet2mri, "out_file_xfm")
workflow.connect(invert_concat_pet2misalign_xfm, "output_file", final_pet2mri, "out_file_xfm_invert")
pet_brain_mask = transform_brainmaskNode
pet_brain_mask_img = 'out_file'
#Resample 4d PET image to T1 space
pettot1_4d = pe.Node(interface=minc.Resample(), name='pettot1_4d')
pettot1_4d.inputs.output_file='pet_space-t1_4d.mnc'
workflow.connect(inputnode, 'pet_volume_4d', pettot1_4d, 'input_file')
workflow.connect(pet2mri, 'out_file_xfm', pettot1_4d, 'transformation')
workflow.connect(inputnode, 'nativeT1nuc', pettot1_4d, 'like')
#Resample 4d PET image to MNI space
PETMNIXfm_node = pe.Node( interface=ConcatCommand(), name="PETMNIXfm_node")
workflow.connect(pet2mri, "out_file_xfm", PETMNIXfm_node, "in_file")
workflow.connect(inputnode, "xfmT1MNI", PETMNIXfm_node, "in_file_2")
MNIPETXfm_node = pe.Node(interface=minc.XfmInvert(), name="MNIPETXfm_node")
workflow.connect( PETMNIXfm_node, "out_file", MNIPETXfm_node, 'input_file' )
t1tomni_4d = pe.Node(interface=minc.Resample(), name='t1tomni_4d')
workflow.connect(pettot1_4d, 'output_file', t1tomni_4d, 'input_file')
workflow.connect(inputnode, "xfmT1MNI", t1tomni_4d, 'transformation')
workflow.connect(inputnode, 'T1Tal', t1tomni_4d, 'like')
workflow.connect(PETMNIXfm_node, 'out_file', outputnode, 'petmni_xfm' )
workflow.connect(MNIPETXfm_node, 'output_file', outputnode, 'mnipet_xfm' )
workflow.connect(pettot1_4d,'output_file', outputnode, 'petmri_img_4d')
workflow.connect(t1tomni_4d,'output_file', outputnode, 'petmni_img_4d')
workflow.connect(final_pet2mri, 'out_file_xfm', outputnode, 'petmri_xfm')
workflow.connect(final_pet2mri, 'out_file_xfm_invert', outputnode, 'mripet_xfm')
workflow.connect(final_pet2mri, 'out_file_img', outputnode, 'petmri_img')
workflow.connect(pet_brain_mask, pet_brain_mask_img, outputnode,'pet_brain_mask' )
return workflow
def _run_interface(self, runtime):
#tmpDir = tempfile.mkdtemp()
tmpDir = os.getcwd() + os.sep + 'tmp_PETtoT1LinRegRunning' #tempfile.mkdtemp()
os.mkdir(tmpDir)
source = self.inputs.in_source_file
target = self.inputs.in_target_file
s_base = basename(os.path.splitext(source)[0])
t_base = basename(os.path.splitext(target)[0])
if not isdefined(self.inputs.out_file_xfm):
self.inputs.out_file_xfm = os.getcwd()+os.sep+s_base+self._suffix+'.xfm'
if not isdefined(self.inputs.out_file_xfm_invert):
self.inputs.out_file_xfm_invert = os.getcwd()+os.sep+t_base+self._suffix+'.xfm'
if not isdefined(self.inputs.out_file_img):
self.inputs.out_file_img = os.getcwd()+os.sep+s_base+self._suffix+ '.mnc'
#print("\n\n\n")
#print( self.inputs.out_file_img )
#print("\n\n\n")
#exit(0)
prev_xfm = None
if self.inputs.init_file_xfm:
prev_xfm = self.inputs.init_file_xfm
source = self.inputs.in_source_file
target = self.inputs.in_target_file
s_base = basename(os.path.splitext(source)[0])
t_base = basename(os.path.splitext(target)[0])
if self.inputs.in_source_mask and self.inputs.in_target_mask:
if os.path.isfile(self.inputs.in_source_mask):
source = tmpDir+"/"+s_base+"_masked.mnc"
#run_calc = CalcCommand();
run_calc = minc.Calc();
#MIC run_calc.inputs.in_file = [self.inputs.in_source_file, self.inputs.in_source_mask]
run_calc.inputs.input_files = [self.inputs.in_source_file, self.inputs.in_source_mask]
#MIC run_calc.inputs.out_file = source
run_calc.inputs.output_file = source
print 'Source Mask:', source
# run_calc.inputs.expression='if(A[1]>0.5){out=A[0];}else{out=A[1];}'
run_calc.inputs.expression='A[1] > 0.5 ? A[0] : A[1]'
if self.inputs.verbose:
print run_calc.cmdline
if self.inputs.run:
run_calc.run()
if os.path.isfile(self.inputs.in_target_mask):
target = tmpDir+"/"+t_base+"_masked.mnc"
run_calc.inputs.input_files = [self.inputs.in_target_file, self.inputs.in_target_mask]
#run_calc.inputs.out_file = target
run_calc.inputs.output_file = target
print 'Target Mask:', target
run_calc.inputs.expression='A[1] > 0.5 ? A[0] : A[1]'
if self.inputs.verbose:
print run_calc.cmdline
if self.inputs.run:
run_calc.run()
class conf:
def __init__(self, type_, est, blur_fwhm_target, blur_fwhm_source, steps, tolerance, simplex, lsq, blur_gradient):
self.type_=type_
self.est=est
self.blur_fwhm_target=blur_fwhm_target
self.blur_fwhm_source=blur_fwhm_source
self.steps=steps
self.tolerance=tolerance
self.simplex=simplex
self.lsq=lsq
self.blur_gradient=blur_gradient
if isdefined( self.inputs.lsq ) :
lsq0=self.inputs.lsq
lsq1=self.inputs.lsq
lsq2=self.inputs.lsq
lsq3=self.inputs.lsq
lsq4=self.inputs.lsq
else :
lsq0="lsq6"
lsq1="lsq6"
lsq2="lsq7"
lsq3="lsq9"
lsq4="lsq12"
#conf1 = conf("blur", "-est_translations", 10, 6, "8 8 8", 0.01, 8, lsq1)
#conf2 = conf("blur", "", 6, 6, "4 4 4", 0.004, 6, lsq2)
#conf3 = conf("blur", "", 4, 4, "2 2 2", 0.002, 4, lsq3)
conf0 = conf("blur", "-est_translations", 16, 16, "8 8 8", 0.01, 32, lsq0, False)
conf1 = conf("blur", "", 8, 8, "4 4 4", 0.004, 16, lsq1, False)
conf2 = conf("blur", "", 4, 4, "4 4 4", 0.004, 8, lsq2, False)
conf3 = conf("blur", "", 4, 4, "4 4 4", 0.004, 4, lsq3, True)
conf4 = conf("blur", "", 2, 2, "2 2 2", 0.004, 2, lsq4, True)
#conf_list = [ conf0 ] #, conf1, conf2, conf3, conf4 ]
conf_list = [ conf0, conf1, conf2, conf3, conf4 ]
i=1
for confi in conf_list:
tmp_source=tmpDir+"/"+s_base+"_fwhm"+str(confi.blur_fwhm_source)
tmp_source_blur_base=tmpDir+"/"+s_base+"_fwhm"+str(confi.blur_fwhm_source)
tmp_source_blur=tmpDir+"/"+s_base+"_fwhm"+str(confi.blur_fwhm_source)+"_"+confi.type_+".mnc"
tmp_target=tmpDir+"/"+t_base+"_fwhm"+str(confi.blur_fwhm_target)
tmp_target_blur_base=tmpDir+"/"+t_base+"_fwhm"+str(confi.blur_fwhm_target)
tmp_target_blur=tmpDir+"/"+t_base+"_fwhm"+str(confi.blur_fwhm_target)+"_"+confi.type_+".mnc"
tmp_xfm = tmpDir+"/"+t_base+"_conf"+str(i)+".xfm";
tmp_rspl_vol = tmpDir+"/"+s_base+"_conf"+str(i)+".mnc";
print '-------+------- iteration'+str(i)+' -------+-------'
print ' | steps : \t\t'+ confi.steps
print ' | lsq : \t\t'+ confi.lsq
print ' | blur_fwhm_mri : \t'+ str(confi.blur_fwhm_target)
print ' | blur_fwhm_pet : \t'+ str(confi.blur_fwhm_source)
print ' | simplex : \t\t'+ str(confi.simplex)
print ' | source : \t\t'+ tmp_source_blur
print ' | target : \t\t'+ tmp_target_blur
print ' | xfm : \t\t\t'+ tmp_xfm
print ' | out : \t\t\t'+ tmp_rspl_vol
print '\n'
run_smooth = minc.Blur();
run_smooth.inputs.input_file=target
run_smooth.inputs.fwhm=confi.blur_fwhm_target
run_smooth.inputs.output_file_base=tmp_target_blur_base
if confi.blur_gradient :
run_smooth.inputs.gradient=True
print run_smooth.cmdline
run_smooth.run()
run_smooth = minc.Blur();
run_smooth.inputs.input_file=source
run_smooth.inputs.fwhm=confi.blur_fwhm_source
run_smooth.inputs.output_file_base=tmp_source_blur_base
if confi.blur_gradient :
run_smooth.inputs.gradient=True
run_smooth.inputs.no_apodize=True
print run_smooth.cmdline
run_smooth.run()
run_tracc = TraccCommand();
run_tracc.inputs.in_source_file=tmp_source_blur
run_tracc.inputs.in_target_file=tmp_target_blur
run_tracc.inputs.out_file_xfm=tmp_xfm
run_tracc.inputs.objective_func=self.inputs.metric
run_tracc.inputs.steps=confi.steps
run_tracc.inputs.simplex=confi.simplex
run_tracc.inputs.tolerance=confi.tolerance
run_tracc.inputs.est=confi.est
run_tracc.inputs.lsq=confi.lsq
if prev_xfm:
run_tracc.inputs.transformation=prev_xfm
if self.inputs.in_source_mask:
run_tracc.inputs.in_source_mask=self.inputs.in_source_mask
if self.inputs.in_target_mask:
run_tracc.inputs.in_target_mask=self.inputs.in_target_mask
print run_tracc.cmdline
if self.inputs.run:
run_tracc.run()
run_resample = minc.Resample();
run_resample.inputs.input_file=source
run_resample.inputs.output_file=tmp_rspl_vol
run_resample.inputs.like=target
run_resample.inputs.transformation=tmp_xfm
if self.inputs.verbose:
print run_resample.cmdline
if self.inputs.run:
run_resample.run()
prev_xfm = tmp_xfm
i += 1
print '\n'
#No need for this because the final xfm file includes the initial one
if isdefined(self.inputs.error):
###Create rotation xfm files based on transform error
transformNode = pe.Node(interface=rsl.param2xfmInterfaceCommand(), name='transformNode')
transformNode.inputs.error = self.inputs.error
###
run_concat = minc.ConcatCommand();
run_concat.inputs.in_file=transformNode.inputs.output_file
run_concat.inputs.in_file_2=tmp_xfm
run_concat.inputs.out_file=self.inputs.out_file_xfm
print run_concat.cmdline
run_concat.run()
tmp_xfm = self.inputs.out_file_xfm
misregister_pet = minc.Resample();
misregister_pet.inputs.input_file=self.inputs.out_file_img
#misregister_pet.inputs.output_file=tmpDir+os.sep+"temp_pet_4d_misaligned.mnc"
misregister_pet.inputs.use_input_sampling=True
misregister_pet.inputs.transformation=self.inputs.out_file_xfm
shutil.copy(self.inputs.output_file, self.inputs.out_file_img)
else :
cmd=' '.join(['cp', tmp_xfm, self.inputs.out_file_xfm])
print(cmd)
shutil.copy(tmp_xfm, self.inputs.out_file_xfm)
#Invert transformation
run_xfmpetinvert = minc.XfmInvert();
run_xfmpetinvert.inputs.input_file = self.inputs.out_file_xfm
run_xfmpetinvert.inputs.output_file = self.inputs.out_file_xfm_invert
if self.inputs.verbose:
print run_xfmpetinvert.cmdline
if self.inputs.run:
run_xfmpetinvert.run()
#if self.inputs.out_file_img:
print '\n-+- Resample 3d PET image -+-\n'
run_resample = minc.Resample();
run_resample.inputs.input_file=self.inputs.in_source_file
run_resample.inputs.output_file=self.inputs.out_file_img
run_resample.inputs.like=self.inputs.in_target_file
run_resample.inputs.transformation=self.inputs.out_file_xfm
print '\n\n', self.inputs.out_file_xfm
print self.inputs.out_file_xfm_invert
print self.inputs.out_file_img, '\n\n'
if self.inputs.verbose:
print run_resample.cmdline
if self.inputs.run:
run_resample.run()
#shutil.rmtree(tmpDir)
return runtime
def get_workflow(name, infosource, opts):
'''
Create workflow to perform PET to T1 co-registration.
1. PET to T1 coregistration with brain masks
2. Transform T1 MRI brainmask and headmask from MNI 152 to T1 native
:param name: Name for workflow
:param infosource: Infosource for basic variables like subject id (sid) and condition id (cid)
:param datasink: Node in which output data is sent
:param opts: User options
:returns: workflow
'''
workflow = pe.Workflow(name=name)
#bnDefine input node that will receive input from outside of workflow
inputnode = pe.Node(niu.IdentityInterface(fields=[
"pet_volume", "pet_volume_4d", "nativeT1nuc", "t1_headMask",
"tka_label_img_t1", "results_label_img_t1", "pvc_label_img_t1",
"t1_brain_mask", "xfmT1MNI", "T1Tal", "error", "header"
]),
name='inputnode')
#Define empty node for output
outputnode = pe.Node(niu.IdentityInterface(fields=[
"petmri_img", "pet_img_4d", "petmri_xfm", "mripet_xfm", 'petmni_xfm',
'mnipet_xfm'
]),
name='outputnode')
node_name = "pet_brainmask"
petMasking = pe.Node(interface=PETheadMasking(), name=node_name)
petMasking.inputs.slice_factor = opts.slice_factor
petMasking.inputs.total_factor = opts.total_factor
workflow.connect(inputnode, 'pet_volume', petMasking, 'in_file')
workflow.connect(inputnode, 'header', petMasking, 'in_json')
node_name = "pet2mri"
pet2mri = pe.Node(interface=PETtoT1LinRegRunning(), name=node_name)
pet2mri.inputs.clobber = True
pet2mri.inputs.verbose = opts.verbose
pet2mri.inputs.lsq = "lsq6"
pet2mri.inputs.metric = "mi"
workflow.connect([
(inputnode, pet2mri, [('pet_volume', 'in_source_file')]),
(inputnode, pet2mri, [('nativeT1nuc', 'in_target_file')]) #,
])
if opts.test_group_qc: misalign_pet(workflow, inputnode, pet2mri)
PETMNIXfm_node = pe.Node(interface=ConcatCommand(), name="PETMNIXfm_node")
workflow.connect(pet2mri, "out_file_xfm", PETMNIXfm_node, "in_file")
workflow.connect(inputnode, "xfmT1MNI", PETMNIXfm_node, "in_file_2")
MNIPETXfm_node = pe.Node(interface=minc.XfmInvert(), name="MNIPETXfm_node")
workflow.connect(PETMNIXfm_node, "out_file", MNIPETXfm_node, 'input_file')
workflow.connect(PETMNIXfm_node, 'out_file', outputnode, 'petmni_xfm')
workflow.connect(MNIPETXfm_node, 'output_file', outputnode, 'mnipet_xfm')
#Resample 4d PET image to T1 space
if opts.analysis_space == 't1':
pettot1_4d = pe.Node(interface=minc.Resample(), name='pet_t1_4d')
pettot1_4d.inputs.keep_real_range = True
workflow.connect(inputnode, 'pet_volume_4d', pettot1_4d, 'input_file')
workflow.connect(pet2mri, 'out_file_xfm', pettot1_4d, 'transformation')
workflow.connect(inputnode, 'nativeT1nuc', pettot1_4d, 'like')
workflow.connect(pettot1_4d, 'output_file', outputnode, 'pet_img_4d')
workflow.connect(inputnode, 'nativeT1nuc', outputnode,
't1_analysis_space')
elif opts.analysis_space == "stereo":
#Resample 4d PET image to MNI space
pettomni_4d = pe.Node(interface=minc.Resample(), name='pet_mni_4d')
pettomni_4d.inputs.keep_real_range = True
workflow.connect(inputnode, 'pet_volume_4d', pettomni_4d, 'input_file')
workflow.connect(PETMNIXfm_node, "out_file", pettomni_4d,
'transformation')
workflow.connect(inputnode, 'T1Tal', pettomni_4d, 'like')
workflow.connect(pettomni_4d, 'output_file', outputnode, 'pet_img_4d')
workflow.connect(pet2mri, 'out_file_xfm', outputnode, 'petmri_xfm')
workflow.connect(pet2mri, 'out_file_xfm_invert', outputnode, 'mripet_xfm')
workflow.connect(pet2mri, 'out_file_img', outputnode, 'petmri_img')
return workflow
def get_workflow(name, infosource, opts):
'''
Create workflow to produce labeled images.
1. Invert T1 Native to MNI 152 transformation
2. Transform
4. Transform brainmask from MNI 152 to T1 native
5. Create PVC labeled image
6. Create quantification labeled image
7. Create results labeled image
:param name: Name for workflow
:param infosource: Infosource for basic variables like subject id (sid) and condition id (cid)
:param datasink: Node in which output data is sent
:param opts: User options
:returns: workflow
'''
workflow = pe.Workflow(name=name)
out_list = [
"pet_brainmask", "brain_mask", "results_label_img_t1",
"results_label_img_mni"
]
in_list = [
"nativeT1", "mniT1", "brainmask", "pet_header_json", "pet_volume",
"results_labels", "results_label_template", "results_label_img",
'LinT1MNIXfm', "LinPETMNIXfm", "LinMNIPETXfm", "LinT1PETXfm",
"LinPETT1Xfm"
]
if not opts.nopvc:
out_list += ["pvc_label_img_t1", "pvc_label_img_mni"]
in_list += [
"pvc_labels", "pvc_label_space", "pvc_label_img",
"pvc_label_template"
]
if not opts.tka_method == None:
out_list += ["tka_label_img_t1", "tka_label_img_mni"]
in_list += [
"tka_labels", "tka_label_space", "tka_label_template",
"tka_label_img"
]
#Define input node that will receive input from outside of workflow
inputnode = pe.Node(niu.IdentityInterface(fields=in_list),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=out_list),
name='outputnode')
#Define empty node for output
MNIT1 = pe.Node(interface=minc.XfmInvert(), name="MNIT1")
workflow.connect(inputnode, 'LinT1MNIXfm', MNIT1, 'input_file')
MNIPET = pe.Node(interface=minc.XfmInvert(), name="MNIPET")
workflow.connect(inputnode, 'LinPETMNIXfm', MNIPET, 'input_file')
if not opts.nopvc and not opts.pvc_method == None:
pvc_tfm_node, pvc_tfm_file, pvc_tfm_to, pvc_target_file = get_transforms_for_stage(
MNIT1, MNIPET, inputnode, opts.pvc_label_space,
opts.analysis_space)
if not opts.tka_method == None:
tka_tfm_node, tka_tfm_file, tka_tfm_to, tka_target_file = get_transforms_for_stage(
MNIT1, MNIPET, inputnode, opts.tka_label_space,
opts.analysis_space)
results_tfm_node, results_tfm_file, results_tfm_to, results_target_file = get_transforms_for_stage(
MNIT1, MNIPET, inputnode, opts.results_label_space,
opts.analysis_space)
brain_mask_tfm_node, brain_mask_tfm_file, brain_mask_tfm_to, brain_mask_target_file = get_transforms_for_stage(
MNIT1, MNIPET, inputnode, 'stereo', 'pet')
###################
# Brain Mask Node #
###################
if opts.analysis_space != "stereo":
brain_mask_node = pe.Node(minc.Resample(), "brain_mask_node")
brain_mask_node.inputs.nearest_neighbour_interpolation = True
#brain_mask_node.inputs.output_file="brain_mask_space-"+opts.analysis_space+".mnc"
workflow.connect(inputnode, "brainmask", brain_mask_node, "input_file")
if opts.analysis_space == "t1":
workflow.connect(MNIT1, "output_file", brain_mask_node,
"transformation")
like_file = "nativeT1"
workflow.connect(inputnode, "nativeT1", brain_mask_node, "like")
elif opts.analysis_space == "pet":
workflow.connect(MNIPET, "output_file", brain_mask_node,
"transformation")
workflow.connect(inputnode, "pet_volume", brain_mask_node, "like")
like_file = "pet_volume"
else:
print("Error: Analysis space must be one of pet,stereo,t1 but is",
opts.analysis_space)
exit(1)
else:
brain_mask_node = pe.Node(
niu.IdentityInterface(fields=["output_file"]), "brain_mask")
workflow.connect(inputnode, "brainmask", brain_mask_node,
"output_file")
like_file = "mniT1"
resultsLabels = pe.Node(interface=Labels(), name="resultsLabels")
resultsLabels.inputs.analysis_space = opts.analysis_space
resultsLabels.inputs.label_type = opts.results_label_type
resultsLabels.inputs.space = opts.results_label_space
resultsLabels.inputs.erode_times = opts.results_erode_times
resultsLabels.inputs.brain_only = opts.results_labels_brain_only
resultsLabels.inputs.ones_only = opts.results_labels_ones_only
workflow.connect(inputnode, 'results_labels', resultsLabels, 'labels')
workflow.connect(inputnode, 'results_label_img', resultsLabels,
'label_img')
workflow.connect(inputnode, 'results_label_template', resultsLabels,
'label_template')
workflow.connect(inputnode, like_file, resultsLabels, 'like_file')
workflow.connect(brain_mask_node, "output_file", resultsLabels,
'brainmask')
workflow.connect(results_tfm_node, results_tfm_file, resultsLabels,
"LinXfm")
if not opts.nopvc and not opts.pvc_method == None:
pvcLabels = pe.Node(interface=Labels(), name="pvcLabels")
pvcLabels.inputs.analysis_space = opts.analysis_space
pvcLabels.inputs.label_type = opts.pvc_label_type
pvcLabels.inputs.space = opts.pvc_label_space
pvcLabels.inputs.erode_times = opts.pvc_erode_times
pvcLabels.inputs.brain_only = opts.pvc_labels_brain_only
pvcLabels.inputs.ones_only = opts.pvc_labels_ones_only
workflow.connect(inputnode, 'pvc_labels', pvcLabels, 'labels')
workflow.connect(inputnode, 'pvc_label_img', pvcLabels, 'label_img')
workflow.connect(inputnode, 'pvc_label_template', pvcLabels,
'label_template')
workflow.connect(inputnode, like_file, pvcLabels, 'like_file')
workflow.connect(brain_mask_node, "output_file", pvcLabels,
'brainmask')
workflow.connect(pvc_tfm_node, pvc_tfm_file, pvcLabels, "LinXfm")
if not opts.tka_method == None:
tkaLabels = pe.Node(interface=Labels(), name="tkaLabels")
tkaLabels.inputs.analysis_space = opts.analysis_space
tkaLabels.inputs.label_type = opts.tka_label_type
tkaLabels.inputs.space = opts.tka_label_space
tkaLabels.inputs.erode_times = opts.tka_erode_times
tkaLabels.inputs.brain_only = opts.tka_labels_brain_only
tkaLabels.inputs.ones_only = opts.tka_labels_ones_only
workflow.connect(inputnode, 'tka_labels', tkaLabels, 'labels')
workflow.connect(inputnode, 'tka_label_img', tkaLabels, 'label_img')
workflow.connect(inputnode, 'tka_label_template', tkaLabels,
'label_template')
workflow.connect(inputnode, like_file, tkaLabels, 'like_file')
workflow.connect(brain_mask_node, "output_file", tkaLabels,
'brainmask')
workflow.connect(tka_tfm_node, tka_tfm_file, tkaLabels, "LinXfm")
#workflow.connect(brain_mask_node,"output_file", outputnode, 'brain_mask')
return (workflow)
def get_workflow(name, opts):
workflow = pe.Workflow(name=name)
in_fields = ['t1']
if opts.user_brainmask :
in_fields += ['brain_mask_mni']
if opts.user_t1mni :
in_fields += ['xfmT1MNI']
print("In Fields:", in_fields)
label_types = [opts.tka_label_type, opts.pvc_label_type, opts.results_label_type]
stages = ['tka', 'pvc', 'results']
label_imgs= [opts.tka_label_img, opts.results_label_img, opts.pvc_label_img ]
inputnode = pe.Node(niu.IdentityInterface(fields=in_fields), name="inputnode")
out_fields=['xfmMNIT1', 'xfmT1MNI', 'xfmT1MNI_invert', 'brain_mask_mni', 'brain_mask_t1', 't1_mni', 't1_nat' ]
for stage, label_type in zip(stages, label_types):
print( stage, label_type )
if 'internal_cls' == label_type :
out_fields += [ stage+'_label_img']
print( stage+'_label_img' )
outputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name='outputnode')
#
# Setup dir for minc beast if not using user provided brain mask
#
if not opts.user_brainmask :
if opts.beast_library_dir == None :
library_dir = mincbeast_library(opts.template)
else :
library_dir = opts.beast_library_dir
template_rsl = create_alt_template(opts.template, library_dir)
##########################################
# T1 spatial (+ intensity) normalization #
##########################################
if not opts.user_t1mni:
if opts.coreg_method == 'ants' :
mri2template = pe.Node(interface=mincANTSCommand(args='--float',
collapse_output_transforms=True,
fixed_image=opts.template,
initial_moving_transform_com=True,
num_threads=1,
output_inverse_warped_image=True,
output_warped_image=True,
sigma_units=['vox']*3,
transforms=['Rigid', 'Affine', 'SyN'],
terminal_output='file',
winsorize_lower_quantile=0.005,
winsorize_upper_quantile=0.995,
convergence_threshold=[1e-08, 1e-08, -0.01],
convergence_window_size=[20, 20, 5],
metric=['Mattes', 'Mattes', ['Mattes', 'CC']],
metric_weight=[1.0, 1.0, [0.5, 0.5]],
number_of_iterations=[[10000, 11110, 11110],
[10000, 11110, 11110],
[100, 30, 20]],
radius_or_number_of_bins=[32, 32, [32, 4]],
sampling_percentage=[0.3, 0.3, [None, None]],
sampling_strategy=['Regular',
'Regular',
[None, None]],
shrink_factors=[[3, 2, 1],
[3, 2, 1],
[4, 2, 1]],
smoothing_sigmas=[[4.0, 2.0, 1.0],
[4.0, 2.0, 1.0],
[1.0, 0.5, 0.0]],
transform_parameters=[(0.1,),
(0.1,),
(0.2, 3.0, 0.0)],
use_estimate_learning_rate_once=[True]*3,
use_histogram_matching=[False, False, True],
write_composite_transform=True),
name="mincANTS_registration")
mri2template.inputs.write_composite_transform=True
workflow.connect(inputnode, 't1', mri2template, 'moving_image')
t1_mni_file = 'warped_image'
t1_mni_node=mri2template
tfm_node= mri2template
tfm_file='composite_transform'
else :
mri2template = pe.Node(interface=beast_normalize_with_conversion(), name="mri_normalize")
template_name = os.path.splitext(os.path.basename(template_rsl))[0]
template_dir = os.path.dirname(opts.template)
mri2template.inputs.modelname = template_name
mri2template.inputs.modeldir = template_dir
workflow.connect(inputnode, 't1', mri2template, 'in_file')
t1_mni_file = 'out_file_vol'
t1_mni_node=mri2template
tfm_node= mri2template
tfm_file='out_file_xfm'
else :
transform_t1 = pe.Node(interface=minc.Resample(), name="transform_t1" )
transform_t1.inputs.two=True
workflow.connect(inputnode, 't1', transform_t1, 'input_file')
workflow.connect(inputnode, 'xfmT1MNI', transform_t1, 'transformation')
transform_t1.inputs.like = opts.template
t1_mni_node = transform_t1
t1_mni_file = 'output_file'
tfm_node = inputnode
tfm_file = 'xfmT1MNI'
#
# Invert transformation from T1 to MNI space
#
xfmMNIT1 = pe.Node(interface=minc.XfmInvert(), name="MNIT1")
workflow.connect(tfm_node, tfm_file, xfmMNIT1 , 'input_file')
#
# T1 in native space will be part of the APPIAN target directory
# and hence it won't be necessary to link to the T1 in the source directory.
#
copy_t1_nat = pe.Node(interface=copyCommand(), name="t1_nat" )
workflow.connect(inputnode, 't1', copy_t1_nat, 'input_file')
####################
# T1 Brain masking #
####################
if not opts.user_brainmask :
#Brain Mask MNI-Space
t1MNI_brain_mask = pe.Node(interface=mincbeast(), name="t1_mni_brain_mask")
t1MNI_brain_mask.inputs.library_dir = library_dir
t1MNI_brain_mask.inputs.configuration = t1MNI_brain_mask.inputs.library_dir+os.sep+"default.2mm.conf"
t1MNI_brain_mask.inputs.same_resolution = True
t1MNI_brain_mask.inputs.median = True
t1MNI_brain_mask.inputs.fill = True
#t1MNI_brain_mask.inputs.voxel_size=opts.beast_voxel_size
t1MNI_brain_mask.inputs.median = opts.beast_median
workflow.connect(t1_mni_node, t1_mni_file, t1MNI_brain_mask, "in_file" )
brain_mask_node = t1MNI_brain_mask
brain_mask_file = 'out_file'
else :
brain_mask_node = inputnode
brain_mask_file = 'brain_mask_mni'
#
# Transform brain mask from stereotaxic to T1 native space
#
transform_brain_mask = pe.Node(interface=minc.Resample(), name="transform_brain_mask" )
transform_brain_mask.inputs.nearest_neighbour_interpolation = True
transform_brain_mask.inputs.invert_transformation = True
workflow.connect(brain_mask_node, brain_mask_file, transform_brain_mask, 'input_file')
workflow.connect(inputnode, 't1', transform_brain_mask, 'like')
workflow.connect(tfm_node, tfm_file, transform_brain_mask, 'transformation')
###################################
# Segment T1 in Stereotaxic space #
###################################
seg=None
for stage, label_type, img in zip(stages, label_types, label_imgs) :
print(img, seg)
if 'antsAtropos' == img and seg == None :
seg = pe.Node(interface=mincAtroposCommand(), name="segmentation_ants")
seg.inputs.dimension=3
seg.inputs.number_of_tissue_classes=3 #... opts.
seg.inputs.initialization = 'Otsu'
workflow.connect(t1_mni_node, t1_mni_file, seg, 'intensity_images' )
workflow.connect(brain_mask_node, brain_mask_file, seg, 'mask_image' )
if 'antsAtropos' == img :
workflow.connect(seg, 'classified_image', outputnode, stage+'_label_img')
###############################
# Pass results to output node #
###############################
workflow.connect(brain_mask_node, brain_mask_file, outputnode, 'brain_mask_mni')
workflow.connect(tfm_node, tfm_file, outputnode, 'xfmT1MNI' )
workflow.connect(xfmMNIT1, 'output_file', outputnode, 'xfmMNIT1' )
workflow.connect(transform_brain_mask, 'output_file', outputnode, 'brain_mask_t1')
workflow.connect(t1_mni_node, t1_mni_file, outputnode, 't1_mni')
workflow.connect(copy_t1_nat, 'output_file', outputnode, 't1_nat')
return(workflow)